Expression profiling by array Expression profiling by genome tiling array
Summary
Identify transcriptionally-active regions (TARs) greater than 400 nt long across the entire human genome. A total of 578 were identified in NHBE cells. We then focused on those TARs originating from non-coding sequence and that displayed a moderate to high degree of sequence conservation. A subset of 15 non-coding transcripts were then further examined to determine if they are altered in cancer (deregulated expression in breast and ovarian cancer and sequenced for mutations in a panel of cancer samples). Only transcriptionally-active regions originating from non-coding sequence, expressing at the 99.5th percentile, and longer than 400 nt were examined so far in our studies. Keywords: whole-genome mapping, transcriptionally-active regions, tiling arrays, non-coding transcripts, bronchial/tracheal epithelial cells
Overall design
Total RNA isolated from NHBE cell cultures were labeled and hybridized to 3 sets of the GeneChip® Human Tiling 1.0R Array set of 14 (3 x 14 = 49 chips total) according to supplier's protocol. A total of 3 biological replicates were run. Each biological replicate was run on an entire set of 14 chips which covers the entire non-repetitive portion of the human genome. The first 2 sets were labeled and hybridized together and the 3rd set was hybridized at a later date. Also, for the first 2 tiling array sets, ribosomal RNA removal was not part of the initial protocol. However, since we ran the 3rd set at a later date the protocol changed and included a ribosomal removal step.
99.5 percentile tiling data: signal values in the 99.5th percentile of the tiling data and longer 400 nt in length, data averages of the three replicates are displayed below for each sample (chip 01 to chip 14). The location (chromosome, start and stop coordinates) of signals and transcript size (length of consecutive probes with signal in the 99.5th percentile) are displayed for each samples tested. header descriptions
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